http://mheironimus.blogspot.gr/2015/09/linux-support-for-arduino-leonardo.html

Solution Found! For anyone else having problems with Leonardo/Micro problems, it's just a matter of adding a string to the end of the line in /boot/cmdline.txt depending on your setup:

usbhid.quirks=0x2341:0x8036:0x040 (for Leonardo)
usbhid.quirks=0x2341:0x8037:0x040 (for Micro)

Yay!

@ortsac thanks for your answer. I understand and will try to find a way positioning the cable differently, or just live with it :)

Regards.